Stonewall's survey reveals that discrimination within the NHS means gay and bisexual men do not always get a fair hearing from their GP. Photograph: Alamy

Gay and bisexual men are neglected and sometimes discriminated against by a health service that tends to focus solely on their sexual health, despite the fact they are more likely to self-harm, attempt suicide and experience depression, according to a major study.

Almost 6,900 gay and bisexual men across the UK who had used NHS healthcare services in the last year were surveyed by gay rights charity Stonewall. The survey reveals that a third have had a negative experience related to their sexuality. Confidence in confidentiality systems and lack of opportunities for discussion were so poor that the same proportion had not even come out to their GP or other staff. The men said they were more likely to be open about their sexual orientation with their manager and work colleagues than with healthcare professionals.

Stonewall's chief executive, Ben Summerskill, says the findings of the report – the largest such study in the world – are "deeply troubling" because the lack of trust may discourage Britain's 1.8 million gay and bisexual men from accessing crucial advice and testing services.

Nearly a third of respondents had never had an HIV test, despite early diagnosis now being a public health priority, and 54% had never discussed HIV with a healthcare professional, the survey reveals.

In the last year, 3% of gay men and 5% of bisexual men had tried to kill themselves compared with 0.4% of all men. Over the same period, 7% of gay and bisexual men had deliberately harmed themselves, compared with just 3% of all men.

Mental health issues were even more acute among younger gay and bisexual men: of those aged 16 to 24, 6% had tried to take their own life in the last year and 15% had harmed themselves. Domestic abuse was another serious problem: half of those surveyed had experienced at least one incident from a family member or partner since the age of 16, compared with 17% of all men.

The report lays bare discrimination in the health service. "I overheard the reception staff say to a nurse: 'The poof is here for his appointment,'" David, 23, told Stonewall. Jack, 37, described how his doctor wrote "homosexual" in capital letters on a letter he had to take to hospital after breaking his wrist. Every time a different doctor pulled up his details on the computer, the same tag would appear.

Nathan, 20, said his GP refused to speak with him, ushering him out of the office and telling him to contact the local sexual health clinic instead.

Several respondents talked of health professionals assuming that because they were gay, they must be HIV positive, while others described professionals referring to them having wives or girlfriends, even after they had made it clear they were gay. Some had distressing experiences of their same-sex partner rights being ignored. "My partner is terminally ill with cancer," said Eddie, 52. "Even though he asked for his treatment to be talked over with me and to call me before his family, they have often not done so."

Of the third of respondents who had not been tested for HIV, 70% said it was because they did not think they had put themselves at risk, while a third said it was because they had never had any symptoms of HIV infection.

"These figures raise grave concerns about the effectiveness with which hundreds of millions of pounds of public money have been spent on HIV awareness and prevention in recent years," the report says.

Summerskill adds: "Patients accessing healthcare should be confident that they'll be treated compassionately, confidentially and with complete openness. But this research reveals that for many gay and bisexual men in Britain this is simply not the case."

The report also finds that respondents were more likely to smoke, drink and take illegal drugs. "It ill-serves our gay and bisexual communities when these uncomfortable truths are ignored," says Summerskill.

The report makes a number of recommendations that could help health services improve, from the Royal Colleges updating professional development programmes for their members to include topics such as same-sex partner rights, to frontline staff being trained about the importance of not assuming someone's sexual orientation. Workers should also encourage disclosure by asking open questions and having clear confidentiality policies. Just one in 11 of respondents said they had been given the opportunity to come out.

Policies explicitly protecting gay and bisexual people from discrimination should be displayed at surgeries and hospitals, and improving access to sexual health services for gay and bisexual men should be made a public health priority, the report concludes.

A Department of Health spokeswoman says lesbian, gay and bisexual people are prioritised in its mental health strategy because it recognises "they are at a higher risk of mental health problems, violence and self-harm". She adds that the latest GP Patient Survey shows that 84% of gay, lesbian and bisexual respondents described their overall experience of their GP surgery as "good".